[Biopython-dev] streamerror

Jeffrey Chang jchang at jeffchang.com
Thu Sep 4 02:46:38 EDT 2003

On Wednesday, September 3, 2003, at 09:14  PM, kim750 at ggbio.com wrote:

> Hi!
> This is Yeon-Ki.
> When I run local_blast.py in the biopython package, I have an error 
> message like this:
[... traceback cut]

The "Unexpected end of stream"  exception happens when the parser is 
looking for a line in a file, and it can't find it before the file 
ends.  Either there's a bug in the parser, or there is an error in the 

> I modified instances for path name as abosolute one because all the 
> datafiles are sprayed through the directories. For ex, my_blast_db = 
> os.path.join(absolute path).

This code doesn't look quite right.  os.path.join joins bits of a path 
together to form a complete path for a file.  Are you sure that this is 
generating a correct filename, and the filename it creates is the name 
of the BLAST format file, and not another file?  If the file that it 
creates is not a BLAST format file, it could very well be reading the 
wrong file and cause the error.


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